Transcription profiling of cod to determine whether gene expression profiles would reflect environmental levels and composition of pollutants in two saltwater recipients, Sarfjorden and Store Lungegardsvann
Ontology highlight
ABSTRACT:
ORGANISM(S): Gadus morhua
SUBMITTER: Kai Lie
PROVIDER: E-BASE-11 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Understanding pathogen recognition and mechanisms in Atlantic cod are of significant importance for both basic research on wild populations and health management in aquaculture. A microarray approach was utilized to search for effects of viral (poly I:C/ polyinosinic acid:polycytidylic acid), bacterial (LPS/lipopolysaccharide) and polyclonal activator (PHA-L/phytohaemoagglutinin) stress in Atlantic cod head kidney cells. LPS cell activation increased mRNA expression of chemokine/Interleukin 8 (CXCL8/IL-8); interleukin -1? (IL-1?); cyclooxygenase 2 (COX2); leukocyte derived chemotaxin 2 (LECT2); LOC100698154, encoding a protein with unknown function; carboxyl-esterase 2 (CES2) and environmental biomarker cytochrome P450 1A (CYP1A). Mitogen activated protein kinase p38 (p38MAPK) and cathepsin F (CTSF) were downregulated by LPS. The antiviral responses induced by double stranded RNA (Poly I:C) clearly increased transcription of Toll like receptor 3 (TLR3) and interferon stimulating gene 15 (ISG15). The PHA response seemed to be more non-specific. Special for the PHA induction were the increase in Major histocompatibility complex class I (MHCI). CC chemokine type 2 (CK2) mRNA expression was increased by PHA, LPS and poly I:C, while p38MAPK and LECT2 was downregulated by PHA. Oxidative stress related genes like catalase and glutaredoxin (GLRX2) and the anti-apoptotic gene Bcl-2 showed no transcriptional changes compared to control in any of the treatments. Especially Poly I:C, but also LPS, induced leukotriene B4 (LTB4) and leukotriene B5 (LTB5) synthesis, while small amounts of prostaglandine E2 (PGE2) seemed to be constitutively produced in untreated cells, a production that was slightly elevated when exposing cells for LPS. This study reveals distinct signatures of bacteria and virus transcriptional responses in cod head kidney cells. In addition, the novel finding that Cyp1a was upregulated during the antibacterial response indicates a connection between immunity and aryl hydrocarbon receptor (AhR) activation in Atlantic cod.
2012-03-21 | E-MTAB-1058 | biostudies-arrayexpress
Project description:Female Atlantic cod (Gadus morhua)were devided in to five groups and oraly exposed to alkylphenols and produced water for 20 weeks. Differentially expressed genes were studied in liver samples using the CodStress array. The five groups were fed with feed-paste containing two different doses of the AP mixture (Low AP and High AP), PW, 17?-estradiol (E2) and toxicant-free paste (control group) respectively. The body burden for each compound corresponded to 20 ?g/kg of total AP in Low AP group, 4000 ?g/kg ?g/kg of total AP in High AP group, 100 ?g E2/kg in the E2 group 500 mg PW/kg in the PW group.
2009-03-25 | E-TABM-676 | biostudies-arrayexpress
Project description:This experiment was conducted in order to evaluate the potential contribution of oil droplets to the toxicity of dispersed oil to fish larvae. Atlantic cod larvae were exposed to five concentrations of either dispersed oil (D1-D5) (containing oil droplets [medium size 10-14 µm based on volume] and water soluble fraction [WSF]) or the filtered dispersion containing only WSF of oil (W1-W5) for four days and harvested for transcriptional analysis at 13 days post hatching. The most significant differently expressed genes were observed in cod larvae exposed to the highest concentration of the dispersed oil (containing 10.41 ± 0.46 µg ∑PAH/L), with CYP1A showing the strongest response. Functional analysis further showed that the top scored network as analyzed with Ingenuity Pathway Analysis was “Drug Metabolism, Endocrine System Development and Function, Lipid Metabolism”. Oil exposure also increased the expression of genes involved in bone resorption and decreased the expression of genes related to bone formation. In conclusion, oil exposure affects drug metabolism, endocrine regulation, cell differentiation and proliferation, apoptosis, fatty acid biosynthesis and tissue development in Atlantic cod larvae. The altered gene transcription was dominated by the WSF and the oil droplet fraction only had a moderate impact on the observed changes.
2011-09-01 | E-TABM-1136 | biostudies-arrayexpress
Project description:Atlantic salmon at their 2nd year in sea were fed with a low, medium or high histidine diet (L, M, and H, respectively) for several months. Samples were taken at three time points, after the first, second and third period, and a number of fishes were assigned to a new feed group following a crossover experimental design. The feeding experiment was carried out in duplicates in cages in sea water. A number of 6 fishes of each nutritional group and from each replicate were sampled at each time point, and weight, length and cataract development were monitored of the sampled fish and an additional number of fishes (18-34). Fish developed cataracts with different severity in response to dietary histidine levels. Lens N-acetylhistidine contents reflected the dietary histidine levels and were negatively correlated to cataract scores. This experiment contains four dietary groups of fish, named LM, HM, LLL and MMM. <br>LM: Low histidine diet in the first period, Medium histidine diet in the second period<br>HM: High first, Medium second period<br>LLL: Low diet in all three periods<br>MMM: Medium diet in all three periods<br>In the analysis LM and HM is compared for early effects, while LLL vs MMM is compared for stable long time effects. Each feeding period is roughly a month each. Each dietary group contains 11 biological replicates. The RNA samples were labelled and hybridised to two channel 16K cGRASP salmonid arrays using a common reference design. The common reference was made from a pool of all samples.
2009-03-27 | E-TABM-678 | biostudies-arrayexpress
Project description:This study was conducted to follow up on apparent differences in growth, relative organ sizes, cellular stress and immune function in Atlantic salmon fed genetically modified (GM) Bt-maize compared to the non-modified parental maize line. Gene expression profiling on the distal intestinal segment and liver were performed by the cGRASP 16K salmonid cDNA microarray. Analysis of the intestinal microarray data revealed nearly 500 differentially regulated genes with a false discovery rate of zero, despite modest fold differences (average 2.4 for the down-regulated and 1.7 for the up-regulated genes). However, nine out of ten genes were found not to be significantly different when followed up by quantitative polymerase chain reaction (qPCR), but direction and magnitude of the change was generally confirmed, at least for the up-regulated genes. For the liver microarray data, statistical analyses could not be performed due to constraints in the design. qPCR revealed some differentially regulated genes in the liver, including up-regulation of gelsolin precursor, down-regulation of ferritin heavy subunit and a tendency towards down-regulation of metallothionein B. This, combined with up-regulation of anti-apoptotic protein NR13 and a tendency towards up-regulation of both ferritin heavy chain and metallothionein A and B in the distal intestine, suggests changes in cellular stress/ anti-oxidant status. This corresponds well with, and strengthens previous findings in these fish. To exclude possible confounding factors, the maize ingredients were analyzed for mycotoxins and metabolites, and the GM maize variety contain 90M-NM-<g/kg deoxynivalenol (DON), compared to levels below the detection limit in the non-GM maize. Numerous differences were also seen in the metabolite profiles of the two maize varieties, some of which seem to be connected to the mycotoxin level. The effects on salmon observed in the current and in previous studies correspond relatively well with effects of DON as reported in the literature for other production animals, but knowledge regarding effects and harmful dose levels in fish are practically non-existing, thus it is difficult to conclude whether the observed effects in the fish are caused by the DON level or by some other aspect of the GM maize ingredient.
2010-10-01 | E-TABM-1056 | biostudies-arrayexpress
Project description:22 chemicals on 2 cell lines, 2 concentrations and 2 exposure times, 2 replicates on custom arrays
2007-12-31 | E-TOXM-31 | biostudies-arrayexpress
Project description:Bacteria use small diffusible molecules to communicate and to coordinate population response by a cell density-depend mechanism named quorum sensing (QS). If such a cross-talk was first described between bacterial species, it was recently evidenced that bacterial QS signal molecules can also be sensed by eukaryotic organisms thus playing as inter-kingdom signalling molecules. Although ectomycorrhizal fungi interact physically and metabolically with myriads of bacterial species in soils, nothing is known about the ability of ectomycorrhiza-associated bacteria to produce QS molecules and the potential impact of these molecules in the interaction. While investigating the potential effect of these molecules on the physiology of the ectomycorrhizal fungus, we found that 3O,C12-HSL also induced an alteration of the transcriptome of L. bicolor S238N. This study used the microarray design as follows: cDNA libraries from pure culture of Laccaria bicolor S238N mycelium and from three stages of L. bicolor S238N sporocarp development (Lb2 library: stipes and caps of 5–10 mm growing sporocarps; Lb3 library: caps of 30– 40 mm mature sporocarps), collected under Douglas fir seedlings grown in a glasshouse, were constructed in the λTriplEx2 vector. The cDNA inserts from bacterial clones were PCR-amplified and 4992 cDNAs were arrayed from 384-well microtitre plates on Nylon membranes. Three independent biological replicates were performed for the treatment (3,OC12-HSL) and for the control (ethyl acetate)
2010-11-23 | E-GEOD-18635 | biostudies-arrayexpress
Project description:Expression analysis of cells the given amount of time after mtDNA was lost (or Nar1 expression was repressed) compared to pretreatment (or NAR1 being fully expressed). One time course experiment (Cells a given amount of time following mtDNA loss compared to cells with intact mtDNA), with 2 two condition experiments (Cells with the ATP1-111 genotype 27 hours following mtDNA loss compared to the same cells with intact mtDNA, and cells 27 hours following repression of NAR1 comared to cells expressing NAR1). Each data point had 3 biological replicates, and was dye-swapped. One replicate per array.
2010-06-21 | E-GEOD-15302 | biostudies-arrayexpress
Project description:Background and objective: Combination antiretroviral therapy (cART) is associated with lipodystrophy i.e. loss of subcutaneous adipose tissue in abdomen, limbs and face and its accumulation intra-abdominally. No fat is lost dorsocervically and it can even accumulates in this region (“buffalo hump”). It is unknown how preserved dorsocervical fat differs from abdominal subcutaneous fat in HIV-1-infected cART-treated patients with (cART+LD+) and without (cART+LD-) lipodystrophy. Results: Albeit dorsocervical adipose tissue in cART+LD+ seems spared from lipoatrophy, its mitochondrial DNA (mtDNA, copies/cell) content was significantly lower (by 62%) than that of the corresponding tissue in cART+LD-. Expression of CD68 mRNA, a marker of macrophages, and numerous inflammatory genes in microarray were significantly lower in dorsocervical vs. abdominal subcutaneous adipose tissue. Genes with the greatest difference in expression between the two depots were those involved in regulation of transcription and regionalization (homeobox genes), irrespective of lipodystrophy status. There was negligible mRNA expression of uncoupling protein 1, a gene characteristic of brown adipose tissue, in either depot. Conclusions: As mtDNA is depleted even in the non-atrophic dorsocervical adipose tissue, it is unlikely that the cause of lipoatrophy is loss of mtDNA. Dorsocervical adipose tissue is less inflamed than lipoatrophic adipose tissue. It does not resemble brown adipose tissue. The greatest difference in gene expression between dorsocervical and abdominal s.c. adipose tissue is in expression of homeobox genes. We used histology, microarray, polymerase chain reaction and magnetic resonance imaging to compare dorsocervical and abdominal subcutaneous adipose tissue in cART+LD+ (n=21) and cART+LD- (n=11). The study consists of 17 patients on antiretroviral treatment who have developed lipodystrophy and 11 patients that are on similar treatment but have not developped lipodystrophy. All patients are HIV+ and have 2 adipose tissue samples taken from them (dorsocervical+abdominal).
2011-09-14 | E-GEOD-28073 | biostudies-arrayexpress
Project description:In order to elucidate the molecular mechanisms of action of Phenytoin, we examined by microarrays the effects of prolonged administration of Phenytoin on gene expression in hippocampus and frontal cortex of Sprague-Dawley rats chronically treated with Phenytoin.
2009-12-31 | E-MEXP-1728 | biostudies-arrayexpress